title: NF_MTB_rep2

status: Public on Nov 09 2019

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M.tuberculosis H37Rv genome (GenBank accession code AL123456.3) using bowtie2 v2.3.4.3 with parameters -p 4 --local --dovetail
Fragments counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The files "Counts_XXX.txt" represent these counts (File "Counts_all.csv" contains values for all samples).
Search for differentially expressed genes was done with DESeq2 package (using only CDS transcripts and putative small RNAs). The results are represented in file "DifferentialExpression.csv"
Genome_build: AL123456.3
Supplementary_files_format_and_content: Counts, DifferentialExpression

organism: Mycobacterium tuberculosis

source_name: in vivo infected neutrophils

growth_protocol: To obtain the log-phase bacteria for challenge, 50 µl from a thawed aliquot was added to 30 ml of Dubos broth base (BD) supplemented with 0.5% fatty acid-poor BSA (Calbiochem) and incubated for 2 weeks at 37°C. The resulting suspension was washed two times at 3000 g, 20 min, 4°C with Ca2+- and Mg2+-free PBS containing 0.2 mM EDTA and 0.025% Tween 80, re-suspended in PBS with 0,025% Tween 80 and ﬁltered through a 5 µm-pore-size ﬁlter (Millipore) to remove clumps.

extract_protocol:
Total RNA was isolated by phenol-chloroform extraction after cell disruption with Bead Beater (BioSpec Products).
After isolation, RNA was treated with Turbo DNase (Life Technologies) to remove traces of genomic DNA. RNA samples were depleted of both prokaryotic and eukaryotic rRNA with Ribo-Zero Gold rRNA Removal Kit (Illumina) (Samples NF_MTB_rep 1-3) or RiboMinus Transcriptome Isolation Kit, Bacteria (ThermoFisher) (Samples MTB_control_rep 1-3). Sequencing libraries were generated using the resulting ribosomal transcript-depleted RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturers’ protocol.

treatment_protocol: Mice were injected with 2 ml 3% peptone (Sigma) in saline in peritoneal cavities (i. p.). Four hours later, mice were injected i. p. with 200 × 106 M. tuberculosis H37Rv in 1 ml of Ca2+- and Mg2+-free PBS-0,025% Tween 80.  Two hours later, peritoneal exudate cells (PEC) were aspirated from peritoneal cavities with Ca2+- and Mg2+-free PBS supplemented with 2% FCS and 10 U of heparin/ml. The neutrophil content among PEC was always >90%, as estimated by Giemsa staining.To remove extracellular mycobacteria we employed differential buoyant density: for free mycobacteria = 1.1-1.2 g/ml, for neutrophils associated with mycobacteria <1.09 g/ml.   Isolated PEC were washed at 300 g, 8 min, 4°C with PBS containing 2% FCS, re-suspended in isotonic Percoll Plus solution  (GE Healthcare) to ρ = 1.1 g/ml, over-layered with isotonic Percoll Plus of ρ=1.09 g/ml and pure PBS and centrifuged at 800 g, 20 min, 4°C. The interphase between Percoll 1.09 g/ml and PBS layers was collected, washed once with PBS at 300 g, 8 min, 4°C, re-suspended in 4 ml of deionized water with 1mM EDTA with 0.05% Tween 80 at pH = 6.5, and put into a Dounce homogenizer. After disruption of neutrophils by 10 frictions, the isotonicity of lysate was restored with 4 ml of 2x PBS. Lysates were filtered through a 5 µm-pore-size filter, centrifuged at 3000 g, 20 min, 4°C, and mycobacterial pellet was suspended in 1 ml of Trizol.  For controls pure M. tuberculosis H37Rv cultured in Dubos broth was centrifuged at 3000 g, 20 min, 4°C, and mycobacterial pellet was suspended in 1 ml of Trizol.

tag: strain

value: in vivo neutrophil infection


title: MTB_control_rep3

type: SRA

library_source: transcriptomic

molecule: total RNA

source_name: bacterial culture

tag: condition

value: Dubos broth


title: NF_MTB_rep3


title: MTB_control_rep2


title: scRNA-Seq_17KO /Colon

city: Tianjin

first: Ming

last: Wei

address: 94 Weijin road

department: Department of Immunology, Nankai University School of Medicine

country: China

institute: Nankai University

data_processing:
Initially, raw base call (BCL) files generated by Illumina sequencers was demultiplexed into FASTQ files
After barcode processing, sequencing reads per cell barcode were then aligned to the UCSC mm10 transcriptome with STAR (version 2.5.1b).
Prior to single-cell 3ʹgene counting, duplicates were filtered based on unique molecular identifiers (UMIs), and finally single cell information (gene expression matrix) of each individual sample was generated.
In this study, outputs of samples from different runs of cellranger count were merged together, facilitated by cellranger aggr pipeline which normalized those runs to the same sequencing depth among libraries.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations;

molecule: polyA RNA

organism: Mus musculus

source_name: colonic LP tissues of SPF mice

growth_protocol: Generated lncly6c deficient mice were cultured and maintained in a specific pathogen-free condition

extract_protocol:
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad)  at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: Lncly6c (1700016P04Rik )-deﬁcient mice on a C57BL/6J background were generated by the Model Animal Research Center of Nanjing University (Nanjing, Jiangsu, China) using CRISPR-Cas9 system. Cas9 mRNA and sgRNA were co-injected into zygotes, sgRNA direct Cas9 endonuclease cleavage in upstream of E1 and downstream of E2, and create a DSB(double-strand break). Such breaks were repaired by non-homologous end joining (NHEJ), and resulted in deletion of 1700016P04Rik gene.

tag: cell type

value: colonic LP cells

tag: genotype/variation

value: Lncly6c (1700016P04Rik)-deficient

tag: gender

value: male

tag: age

value: 6-8 weeks


title: scRNA-Seq_WT /Colon

value: wild type


title: D60_PMN_H041_T1_20190709

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

country: USA

institute: University of Maryland School of Medicine

data_processing:
Neisseria gonorrhoeae: Sequence reads were trimmed for adaptor sequence and mapped to the Opaless_3X or H041  Neisseria genomes using bowtie v1.0 with parameters -mode=v --num_mismatches=2 --file-type=fastq --seedlen=28 --minins=0 --maxins=600 --library-type=fr  --args='--sam' --v --gzip
Homo sapiens: Sequenced reads were trimmedfor adaptor sequence and mapped to the 2018 GRCh38 Human genome assembly using HISAT v2.0 with parameters -mismatch-penalties=6,2 --softclip-penalties=2,1 --read-gap-penalties=5,3 --ref-gap-penalties=5,3 --min-intronlen=20 --max-intronlen=500000 --score-min=L,0,-0.2 --pen-cansplice=0 --num-threads=1 --pen-noncansplice=12 --pen-canintronlen=G,-8,1 --pen-noncanintronlen=G,-8,1 --rna-strandness=RF --dta-cufflinks=1 --num-alignments=5 --minins=0 --maxins=600 --no-unal=1 --args='' --v
Neisseria gonorrhoeae: Reads Per Kilobase per Million values for gene features were calculated as described in Shenoy et al. PLoS Pathog. 2017 Aug 25;13(8):e1006582. doi: 10.1371/journal.ppat.1006582. eCollection 2017 Aug.
Homo sapiens: Reads Per Kilobase per Million values for exon features were calculated as described in Shenoy et al. PLoS Pathog. 2017 Aug 25;13(8):e1006582. doi: 10.1371/journal.ppat.1006582. eCollection 2017 Aug.
Genome_build: All data derived from the Opaless and Opaless_3X strains have been mapped to the Opaless_3X genome (GenBank Accession: WHPL00000000), while data derived from the H041 strain have been mapped to the H041 genome (GenBank Accession: WHPH00000000). All human data were mapped to 2018 GRCh38 Human genome assembly.

organism:
Neisseria gonorrhoeae
Homo sapiens

source_name: Neisseria gonorrhoeae strains FA1090 derivatives/H041 and adherent primary human neutrophils, alone and after co-culture over time, with or without prior antibiotic treatment

growth_protocol: N. gonorrhoeae of strain FA1090 or H041/WHOX (Ohnishi et al, Emerg Infect Dis 2011) was grown in GCBL medium containing Kellogg's supplements and sodium bicarbonate for successive rounds of growth in order to enrich for exponentially growing bacteria, as described in Criss AK et al, Cellular Microbiology 2009. FA1090 N. gonorrhoeae were constitutively piliated and deleted for Opa proteins ("Opaless" or 130; Ball and Criss, J Bacteriol 2013). 130 was sequentially transformed with the penA, mtrR, and penB alleles from superbug strain H041 to generate the isogenic antibiotic resistant strain "3X 130". Primary human neutrophils were isolated from the venous blood of healthy human donors by dextran sedimentation followed by Ficoll purification and hypotonic lysis of residual erythrocytes. Neutrophils were placed on tissue culture treated plastic coverslips in RPMI medium containing 10% fetal bovine serum and 10 nM interleukin-8 for 30 minutes to allow for adherence.

extract_protocol:
At indicated times, samples were placed on ice. Bacteria alone were collected into microcentrifuge tubes, pelleted, and stored in RNAprotect at -80C. Supernatants were discarded from neutrophil containing samples, RNA protect was added, and samples were stored at -80C. Samples were exposed to EDTA pre-extraction and during the lysis step. Extractions were performed using Qiagen’s RNeasy extraction kit as per manufacturer’s protocol. An additional Turbo DNase was performed after the final step of RNeasy protocol. Quality and quantity were determined using the Agilent 4200 TapeStation System.
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N. gonorrhoeae was left untreated or exposed to sublethal concentrations of ceftriaxone (0.25 ng/ml for 130, 31.25 ng/ml for 3x130, 62.5 ng/ml for H041), gentamicin (156 ng/ml for 130 and H041, 312.5 ng/ml for 3x130), or azithromycin (6 ng/ml for 130 and H041, 12.5 ng/ml for 3x130) for 1 hour. Bacteria were then added to adherent human neutrophils at MOI = 1 in RPMI + 10% FBS, or inoculated into RPMI + 10% FBS without neutrophils. Incubations were for 0 hour or 1 hour. Antibiotics were kept at the same concentration throughout the experiment.

tag: donor

tag: treatment condition

value: Co-culture

tag: human cell type

value: PMN

tag: incubation time

value: 60 min in medium with PMN

tag: n. gonorrhoeae strain


title: NF_MTB_rep1


title: D60_PMN_H041_T0_20181212

value: 0 min in medium with PMN


title: YE110-1

status: Public on Nov 10 2019

city: San Francisco

first: Meena

last: Subramaniam

state: CA

address: 513 Parnassus Ave S-965

institute: UCSF IHG

description: sle.mtx

data_processing:
10x CellRanger was run on each faw sample with default settings
Demuxlet software was run on each sample with default settings and genotyping parameter 0.1
Counts matrices  from the 10x Cellranger software were aggregated across samples and doublets flagged by Demuxlet were removed
Genome_build: hg19
Supplementary_files_format_and_content: MTX files (count matrices), TXT files (row and column annotations)

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs from SLE patients and healthy controls were Ficoll-isolated and prepared using the 10x Chromium Single cell instrument standard protocol.
10x Chromium Single Cell Workflow
10x Chromium Single Cell Library Prep

value: PBMCs

value: SLE

tag: sample type

value: primary cells

tag: chip antibody


title: D60_PMN_H041_T0_20190709


title: Control 3

type: RNA

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description: circRNA expression data from samples of normal mice

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: RPE-choroid-sclera complexes from normal eye

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: The animals were maintained in cages in temperature-controlled rooms featuring a 12-h light/12-h dark cycle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The photocoagulation was applied in eyes of mice around the optic disc using a 532-nm diode laser (100 mW, 0.1 s duration, 50 μm).  Twenty-five spots were burned on each eye, and the eyes were enucleated at 7 days after the laser photocoagulation. Age-matched mice without laser photocoagulation treatment were used as controls.

tag: tissue

value: RPE-choroid-sclera complexes

tag: disease state

value: normal


title: CNV 2

description: circRNA expression data from sampes of laser-induced CNV mice

source_name: RPE-choroid-sclera complexes from laser-induced CNV eye (7 days after the laser photocoagulation)

value: laser-induced CNV


title: D60_PMN_H041_Gent_T1_20190709

tag: antibiotic

value: Gent


title: CNV 1


title: Control 1


title: D60_PMN_H041_Ceft_T1_20190709

value: Ceft


title: D60_PMN_H041_Gent_T0_20190709


title: MTB_control_rep1

value: Dubos broth


title: Col-0_smallRNA-seq

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were  mapped to TAIR10  genome using bowtie v 1.1.1 with parameters -a -p 4 -f -S -v 0
bedgraph file were generated from High-throughput sequencing reads of bam format
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using bedGraphToBigWig with default parameters.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis materials were all in the Columbia (Col-0) background and grown on Murashige and Skoog (MS) medium at 22°C with 16-h light/8-h dark (long-day conditions).

extract_protocol:
Small RNA was extracted from 12-day-old seedlings, and 18~60 nt small RNA were gel-purified and subjected to the library construction.
libraries were prepared for small RNA-seq

value: Arabidopsis seedlings

tag: genotype


title: 35S-COLDAIR_smallRNA-seq


title: Col-0_stranded-RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR-2.5.2b with parameters   --runThreadN 30 --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8  --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04  --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20  --readFilesCommand zcat --outSAMattrIHstart 0  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical  --alignSoftClipAtReferenceEnds No
bedgraph file were generated from High-throughput sequencing reads of bam format
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using bedGraphToBigWig with default parameters.

extract_protocol:
Total RNA was extracted from 14-day-old seedlings and subjected to the Vazyme VAHTS Total RNA-seq Library Prep Kit for deep sequencing (Vazyme, NR603)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 35S-COLDAIR_stranded-RNA-seq


title: 35S-COLDAIR-rep1_RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR-2.5.2b with parameters  --runThreadN 40 --quantMode TranscriptomeSAM --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 6 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 10 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 20  --readFilesCommand zcat --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignSoftClipAtReferenceEnds No
High-throughput sequencing reads were calculated using cuflink2.0.0 cuffdiff with parameters -p 16 -N
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each Sample

extract_protocol:
Total RNA was extracted from 12-day-old seedlings, and mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads
RNA libraries were prepared for sequencing using standard Illumina protocols


title: D60_PMN_H041_Ceft_T0_20190709


title: Col-0-rep2_RNA-seq


title: Col-0-rep1_RNA-seq


title: HS 6

first: Jiajia

last: Tang

address: No 1 Shuai- fuyuan, Wangfujing

institute: Peking Union Medical College Hospital

description: tRNA

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.
After Illumina quality control, the sequencing reads were 5‘, 3’-adaptor trimmed, and discarded reads (length < 14nt or length > 40nt) with cutadapt , and were recorded in FASTA format.
Trimmed reads in FASTA format are aligned allowing for 1 mismatch only to the mature tRNA sequences,then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
tRF & tiRNA ID will be divided into four parts by the horizontal line, eg: 'tRF-Gly-TCC-001'. The following is a brief description of these fields:(1) tRF or tiRNA, The type of tRF & tiRNA, eg: tRF; (2) amino acid, Type of amino acid, eg: Gly; (3) anticodon, Type of anticodon, eg: TCC; (4) Serial, The serial number of tRF & tiRNA derived from the tRNA of the same anticodon, eg: 001
The differentially expressed tRFs & tiRNAs and miRNAs are screened based on the count value with R package edgeR. Principal Component Analysis(PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed in R or perl environment for statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb, tRFdb
Supplementary_files_format_and_content: text file with abundance

source_name: serum

extract_protocol:
Before the sequencing experiment, we evaluated the integrity and quantity of each RNA sample using and Nano drop TM instrument. Total RNA from patients’ sera were isolated with TRIzol LS Reagent (Life Technologies, USA), following the manufacturer’s protocols. The concentration and purity of RNA can be determined by the NanoDrop®ND-1000. The ratio of A260 to A280 values is a measurement of RNA purity, and it should fall in the range of 1.8 to 2.1. Final RNA preparations were resuspended in RNase-free water and stored at -70°C.
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA  adapters. cDNA was then synthesized and amplified using Illumina’s  proprietary RT primers and amplification primers. Subsequently, ~134-160 bp  PCR amplified fragments were extracted and purified from the PAGE gel. And  finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.

treatment_protocol: Total RNA samples are pretreated to remove some RNA modifications that  interfere with small RNA-seq library construction.

tag: diagnosis

value: healthy

value: serum

tag: Sex

value: female

tag: thyroiditis

value: no


title: HS 5

description: tRNA

value: male


title: 35S-COLDAIR-rep2_RNA-seq


title: HS 4

description: tRNA


title: HS 3

description: tRNA


title: HS 1

description: tRNA


title: NG 6

description: tRNA

value: nodular goiter (NG)

value: yes


title: D60_PMN_3X130_Gent_T0_20190305

value: Co-culture

value: PMN

value: 0 min in medium with PMN


title: D60_PMN_3X130_Gent_T1_20190305

value: 60 min in medium with PMN


title: D60_PMN_H041_T1_20181212


title: D60_PMN_3X130_T0_20190305


title: Control 2

value: RPE-choroid-sclera complexes

value: normal


title: D60_PMN_3X130_Ceft_T1_20190625


title: D60_PMN_3X130_Ceft_T0_20190730


title: D60_PMN_3X130_Azit_T1_20190305

value: Azit


title: NG 4

description: tRNA


title: D60_PMN_3X130_Ceft_T0_20190305

value: Ceft


title: JHOC9 IL-6 KD#58 replicate e

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data from cell culture

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring 14.9.1 (Agilent) using Affymetrix default analysis settings (RMA processing), chips were normalized to 50th percentile, and genes were normalized to average NT values (samples #)

label: biotin

source_name: JHOC9 cells infected with IL-6 knockdown virus #58 replicate e

label_protocol: This project used the GeneChip™ Human Transcriptome Array 2.0 200 ng of total RNA was used as input

growth_protocol: JHOC9 cells were maintained in DMEM/F12 (Gibco, Invitrogen) supplemented with 20% fetal bovine serum (FBS) (Gemini Bio-Products, Sacramento, CA, USA). JHOC5 cells were maintained in DMEM/F12 (Gibco, Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Gemini Bio-Products, Sacramento, CA, USA)

extract_protocol: Phenol/Chloroform

treatment_protocol: Effect of gene knockdown

value: Ovarian clear cell carcinoma

tag: cell line


title: NG 3

description: tRNA


title: NG 2

description: tRNA


title: D60_PMN_3X130_T1_20190305


title: NG 1

description: tRNA


title: D60_PMN_3X130_Azit_T0_20190305


title: D60_PMN_130_T1_20181113

value: Opaless


title: PTC 6

description: tRNA

value: Papillary thyroid cancer (PTC)


title: HS 2

description: tRNA

value: healthy

value: serum


title: PTC 5

description: tRNA

value: female

value: no


title: NG 5

description: tRNA

value: nodular goiter (NG)


title: D60_PMN_130_Gent_T0_20181113

value: Gent


title: PTC 3

description: tRNA

value: male


title: PTC 1

description: tRNA


title: D60_PMN_130_Gent_T1_20181113

value: Co-culture

value: PMN


title: D60_PMN_130_Ceft_T1_20181113

value: 60 min in medium with PMN


title: D60_PMN_130_Azit_T0_20181113

value: 0 min in medium with PMN


title: Z

city: Montreal

first: Marika

last: Sarfati

state: Quebec

address: 900 rue St Denis

country: Canada

institute: CRCHUM

description: HLADR+SIRPa+

data_processing:
Low-quality cells were filtered out from the dataset based on a threshold of having at least 3000 unique genes detected, where a gene was considered detected if it had at least one transcript in at least 3 cells. This filter discarded 86 out of the 414 samples, leaving 328 samples in the dataset. Next, genes which were detected in less than 3 cells were also discarded such that 17866 genes across 328 cells were retained. Four samples having more than 7800 genes were discarded as likely doublets. Additional quality filters included percent mitochondrial and percent ribosomal genes detected in each cells with maximum of 6.5% and 18% accepted respectively, further removing 10 cells from the dataset (Figure S8A). Thus, after basic quality control filtering, 314 cells were retained.
Next, principal component analysis (PCA) was carried out (prcomp function in R), revealing two outlier populations delineated by PC1 (“outliers_PC1”, n=12 cells) and PC5 (“outliers_PC1”, n=8 cells) (Figure S8B). We noted that both “outliers_PC1” and “outliers_PC5” populations had relatively low ribosomal and mitochondrial gene content compared to the rest of the profiled single cells, suggesting that they are not of low quality (Figure S8C). The “outliers_PC5” group also had higher number of genes, but similar number of genes were detected in other cells suggesting that they are not simply doublets (Figures S8B and S8C). While the exact identity of these populations is difficult to pinpoint, examination of the genes that are characteristic for each population revealed that one of them consists of CD66b/CEACAM8+ cells (possible contaminants from the CD66b gate) and the other contained epithelial (EPCAM+) and cytolytic (CD27+) cells (Figure S8D). Since these populations clearly separated away from the populations of interest, and due to their uncertain identity, they were excluded from further analysis. Ultimately, the 294 sequenced cells that passed all QC filters consisted of 73 P1, 55 P2, 66 P3, 52 P4, and 48 Px samples from three patients, with 46 cells from patient x, 114 cells from patient y, and 134 cells from the patient z (Figure 6C).
Potential batch effects arising from the processing of each individual sample were corrected by fitting a linear model with the patient indicator variable and retaining the residual gene expression as described in Villani et al, Science 2017. PCA analysis was then repeated on the remaining dataset of 314-12-8=294 cells and all genes, and the cell loadings for the first 10 principle components were used for unbiased cluster detection (Louvain clustering algorithm performed via the FindClusters method in Seurat package with parameters: k.param=20, resolution-0.8) and visualization in two dimensions (t-distributed stochastic neighbor embedding (t-SNE)) (Figure 6B).
This unsupervised procedure identified six distinct clusters. The 294 sequenced cells were distributed across the 6 clusters, with 14 cells in cluster A, 60 in cluster B, 18 in cluster C, 32 in cluster D, 98 in cluster E, and 72 in cluster F (Figure 6). To find discriminating genes for each of the clusters, we used the area under the receiver-operator curve (AUC) as main criteria – for each cluster, each gene is evaluated for its ability to predict whether cells can correctly be assigned that cluster versus all other clusters (FindAllMarkers function, test.use="roc"). Genes were selected as discriminating if they passed all of the following conditions: (1) minimum AUC of 0.75, (2) minimum absolute log fold-change of 1.2, (3) the difference between the percent of cells expressing the gene in the cluster and the percent of expressing cells in all other clusters is greater than 0.5 OR this difference is greater than 0.15 but at least 80% of cells in the cluster express the gene (note that this last condition is intended to capture genes which are more discriminating or very consistently expressed in the cluster of interest). There were 349 genes that satisfied the filtering criteria (Table S3). Upon removing PC1 and PC5 outlier clusters and re-analyzing remaining single cells in principal component space, PC1 and PC2 seemed to best capture the cell identity of cells comprised by cluster D in t-SNE plot reported in Figure 6B. Unlike cells comprised within other clusters defined in Figure 6B by set of discriminating genes that are over-expressed, cells from cluster D were most uniquely defined by a set of genes related to the ubiquitin-proteasome system (UPS) commonly down-regulated. Supplementary Figure S7C reports genes of the UPS that are down-regulated in cells from cluster D with an average log fold change less than -0.5.
Table S2 lists the 294 cells included in scRNAseq analysis
Supplementary_files_format_and_content: counts matrix and transcripts per million (tpm) matrix Excel (.xlsx) files

source_name: colonic mucosa

extract_protocol:
Single-cells lysates were thawed on ice for 2 minutes, then centrifuged at 2,500rpm at 4°C for 1 minute. Lysates were mixed with 22µL (2.2X) of Agencourt RNAClean XP SPRI beads (Beckman-Coulter) and incubated at room temperature for 10 minutes. The 96-well plate was then moved onto a magnet (DynaMag-96 Side Skirted Magnet, Life Technologies) for 5 minutes. Supernatant was subsequently removed, and SPRI beads were washed three times using 100µL of freshly prepared 80% ethanol, with care being taken to avoid loss of beads during the washes. Upon completely removing remaining traces of ethanol, SPRI beads were left to dry at room temperature for 10 minutes followed by resuspension in elution mix for reverse transcription reaction.
Library preparation was carried out using the Nextera XT DNA Sample Kit (Illumina) with custom indexing adapters, allowing 384 single cell libraries to be simultaneously generated in a 384-well PCR plate (Eppendorf). For each library, the amplified cDNA was normalized to a 0.15-0.20ng/µL concentration range. The tagmentation reaction consisted of mixing 0.625µL of normalized cDNA with 1.25µL of Tagmentation DNA (TD) Buffer and 0.625µL of Amplicon Tagment enzyme Mix (ATM). The 2.5µL reaction was incubated at 55°C for 10 minutes and then immediately placed on ice upon completing this incubation step. The reaction was quenched with 0.625µL of Neutralize Tagment (NT) Buffer and incubated at room temperature for 10 minutes. The libraries were amplified by adding 1.875µL of Nexstera PCR Master (NPM) Mix, 0.625µL of 10µM i5 adapter (5’-AATGATACGGCGACCACCGAGATCTACAC[i5]TCGTCGGCAGCGTC-3’, IDT, where [i5] signifies the 8 bp i5 barcode sequence (see below for sequences)), and 0.625µL of 10µM i7 adapter (5’CAAGCAGAAGACGGCATACGAGAT[i7] GTCTCGTGGGCTCGG -3’, IDT, where [i7] represents the reverse-complement of the 8 bp i7 barcode sequence (see below for sequences)). The PCR was carried out at an initial incubation at 72°C for 3 minutes, 95°C for 30 seconds, followed by 12 cycles of (95°C for 10 seconds, 55°C for 30 seconds, 72°C for 1 minute), and a final extension at 72°C for 5 minutes. Following PCR amplification, 2.5µL of each library were pooled together in a 2.0 mL Eppendorf tube. The pool was mixed with 864µL (0.9X ratio for 2.5ul of 384 cells pooled together) of Agencourt AMPureXP SPRI beads (Beckman-Coulter) and incubated at room temperature for 5 minutes. The pool was then placed on a magnet (DynaMag-2, Life Technologies) and incubated for 5 minutes. The supernatant was removed and the SPRI beads were washed twice with 1mL of freshly prepared 70% ethanol. Upon removing all residual ethanol traces, the SPRI beads were left to dry at room temperature for 10 minutes. The beads were resuspended in 100µL of nuclease-free water and incubated at room temperature for 5 minutes. The tube was then placed back on the magnet for 3 minutes prior to transferring the supernatant to a new 1.5mL Eppendorf tube. This SPRI clean-up procedure of the library was repeated a second time to remove all residual primer dimers, using the same approach. The concentration of the pooled libraries was measured using the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies/Thermo Fisher Scientific), and the library size distribution measured on a High-Sensitivity Bioanalyzer Chip (Agilent). Expected size distribution of 300-700bp. Pooled samples were sequenced as paired-end on a NextSeq 500 sequencing system (Illumina) using the 75 cycles NextSeq 500/550 High Output kit v2 (catalog number FC-404-2005). i5 barcodes: AAGTAGAG, ACACGATC, CTCTACTT, TCCTTGGT, TGTTCCGA    i7 barcodes: AGTTGCTT, AATGTTCT, CACATCCT, AAGACACT, TGTCGGAT, TCGCCTTG, AGCAATTC, TCTCGGTC, AACTTGAC, ACTAAGAC, AGGTGCGA

tag: cell phenotype

value: HLalphaDR+SIRPalpha+


title: D6_PMN_H041_Gent_T1_20190122


title: D60_PMN_130_Ceft_T0_20181113


title: D60_PMN_130_T0_20181113


title: X

description: HLADR+SIRPa+


title: D60_PMN_130_Azit_T1_20181113

value: Azit


title: D6_PMN_H041_T0_20190122


title: RNA-seq_HUVEC

city: Seoul

first: JaeJun

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using bbmap), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: hDFs transduced with rtTA and tet-HA-ETV2

growth_protocol: hDFs were cultured in EGM-2 (Lonza) supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: After 2 days of doxycycline treatment, DMSO (0.02%) or 5 µM forskolin was supplemented in the medium.

tag: stimulation

tag: cell type

value: HUVEC


title: RNA-seq_Fsk+Dox

value: with doxycycline and Forskolin, day 7

value: induced endothelial cells


title: RNA-seq_CTL-Dox

value: without doxycycline, day 7


title: RNA-seq_Veh+Dox

value: with doxycycline and DMSO, day 7


title: D6_PMN_H041_Ceft_T1_20190122

tag: donor

tag: treatment condition

value: Ceft


title: D6_PMN_H041_Gent_T0_20190122

tag: human cell type

tag: incubation time


title: ChIP-seq_HA_Veh +Dox

library_source: genomic

data_processing:
The reads were trimmed and uniquely mapped to human reference genome (hg19) using Bowtie2.
After duplicated reads were removed, we used model-based analysis of ChIP-seq (MACS2) peak caller to identify peaks against its corresponding input with q value cutoff 0.01.
Any peak in CTL -Dox group that overlapped a peak in +Dox group was removed for analyses.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities.

molecule: genomic DNA

extract_protocol:
Formaldehyde was added to culture medium at a final concentration of 1% and cells were incubated for 10 minutes at 37°C. Then glycine was added at a final concentration of 125 mM to the media, followed by washing with cold PBS containing protease inhibitors twice. The cells were harvested by scraping with Farnham lysis buffer (5 mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) and collected by centrifugation. Cell lysates were resuspended with SDS lysis buffer and incubated for 10 minutes on ice. DNAs in lysates were sheared into 100 to 500 base pairs by sonication and sheared chromatin was purified by centrifugation (15000 x g, 4°C, 10 minutes). After calculation of DNA concentration, 1% of sheared chromatin was stored at -20°C as input. To precipitate chromatin, antibody against HA (901501, BioLegend) was added to the supernatant fraction and incubated overnight at 4°C. By incubation with Protein A Agarose/Salmon Sperm DNA for an hour, unbound DNA was removed, and HA-bound complex was collected. To reverse protein-DNA crosslinking, the solution and stored input were incubated with 5M NaCl for 4 hours at 65°C. Additionally, RNase A and Proteinase K were added and incubated for an hour at 45°C. DNAs were purified by PCR purification kit (Invitrogen).
Purified DNAs were subjected to sequencing library preparation using NEBNext® UltraTM DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. The chipped DNA was ligated with adaptors. Then, after purification, PCR reaction was done with adaptor-ligated DNA and index primer. High-throughput sequencing was performed as single-end 75-bp sequencing using NextSeq 500 (Illumina).

treatment_protocol: After 2 days of doxycycline treatment, DMSO (0.02%) was supplemented in the medium.

value: anti-HA (901501, BioLegend)


title: D60_PMN_H041_Azit_T0_20190709

tag: n. gonorrhoeae strain


title: PTC 4

description: tRNA

value: Papillary thyroid cancer (PTC)

value: serum

tag: age

value: female

value: yes


title: Y

description: HLADR+SIRPa+


title: ChIP-seq_INPUT_CTL -Dox

tag: chip antibody


title: D6_PMN_H041_Azit_T1_20190122

value: Co-culture


title: ChIP-seq_INPUT_Veh +Dox


title: D6_PMN_H041_Ceft_T0_20190122

value: PMN


title: D60_PMN_H041_Azit_T1_20190709

value: 60 min in medium with PMN


title: D6_PMN_3X130_T1_20180802


title: Kelly_ASCL1_MWZ5393 [Lab: Look]

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: 20180324_7006.20180324_Kelly_ASCL1_MWZ5393_S5

data_processing:
Aligned using bowtie2 with configuration -p 4  --no-unal --end-to-end --sensitive
BEDGRAPH files were generated using MACS2 -B. ASCL1 samples were normalized by subtracting corresponding background using MACS2 bdgcmp. The BEDGRAPH files were further floored to 0.1.
hg19
Supplementary_files_format_and_content: BEDGRAPH files represent coverage at each basepair; Normalized BEDGRAPH files represent background-subtracted coverage at each basepair

source_name: Neuroblastoma

growth_protocol: Cells were cultured according to the suggested guidelines in RPMI media containing 10% FBS and 1% Penicillin-Streptomycin

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.

value: Kelly

value: neuroblastoma

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: D6_PMN_3X130_T0_20180802

value: 0 min in medium with PMN


title: Kelly_LMO1_R1_MWZ5393 [Lab: Look]

data_processing:
Aligned using bowtie2 with configuration -p 4  --no-unal --end-to-end --sensitive
BEDGRAPH files were generated using MACS2 -B. LMO1 samples were normalized by subtracting corresponding background using MACS2 bdgcmp. The BEDGRAPH files were further floored to 0.1.
hg19
Supplementary_files_format_and_content: Normalized BEDGRAPH files represent background-subtracted coverage at each basepair (*sort.bedGraph)
Supplementary_files_format_and_content: BEDGRAPH files represent coverage at each basepair (*control.sort.bedGraph)

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog number

tag: antibody lot number


title: Kelly_input_X2_MWZ5393 [Lab: Look]

tag: cell line


title: D6_PMN_3X130_Gent_T1_20190307

tag: antibiotic

value: Gent


title: Kelly_LMO1_X2_MWZ5393 [Lab: Look]


title: Kelly_input_R1_MWZ5393 [Lab: Look]


title: D6_PMN_3X130_T0_20190307


title: D6_PMN_3X130_Azit_T1_20190619

value: Azit


title: D6_PMN_3X130_Ceft_T0_20190307


title: D6_PMN_3X130_Ceft_T1_20190307


title: D6_PMN_3X130_Gent_T0_20190307


title: KZ1334_GB1051-Tgfbr2KO1

city: Bethesda

first: Peter

last: Zanvit

email: peter.zanvit@nih.gov, wailim.ku@nih.gov

state: Maryland

address: 30 Convent Drive

department: NIDCR

institute: NIH

description: 2nd experiment

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
RNA-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 for further analysis in each library.
We computed the rpkm value for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: rpkmtxt: plain text file. The first four lines are information of the files. After these lines, each line is a gene.The four columns are gene, refSeq Accessions, rpkm value, and readcount.

source_name: Bone marrow

extract_protocol:
ILC2 cells were sorted from lamina propria of WT or Tgfbr2-/- mice and RNA was isolated following manufacturer instructions. ILC2p cells were sorted from bone marrow of WT or Tgfbr2-/- mice and RNA was isolated following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tgfbr2f/f ER-cre+ mice were treated with sunflower oil (WT) or tamoxifen (Tgfbr2-) for 5 consecutive days

tag: strain

tag: genotype


title: KZ1334_GB1052-Tgfbr2KO2

description: 2nd experiment

tag: cell type


title: ChIP-seq_HA_CTL -Dox

value: induced endothelial cells

tag: stimulation

value: without doxycycline, day 7


title: D6_PMN_H041_Azit_T0_20190122

tag: donor

tag: treatment condition

tag: human cell type


title: KZ1334_GB1049-WT1

description: 2nd experiment

value: WT


title: KZ1301_GB1036-Tgfbr2KO2

description: 1st experiment


title: KZ1334_GB1050-WT2

description: 2nd experiment


title: KZ1301_GB1035-Tgfbr2KO1

description: 1st experiment


title: D6_PMN_3X130_Azit_T1_20190307

tag: incubation time

tag: n. gonorrhoeae strain


title: D6_PMN_3X130_Azit_T0_20190619


title: D6_PMN_3X130_Azit_T0_20190307


title: KZ1301_GB1034-WT2

description: 1st experiment


title: D6_PMN_130_T1_20181108

value: Opaless


title: D6_PMN_130_T0_20181108


title: D6_PMN_130_Gent_T1_20181108


title: D6_PMN_130_Ceft_T1_20181108

value: Ceft


title: KZ1160_GA9920-Tgfbr2KO

description: 2nd experiment

source_name: Lamina propria


title: KZ1160_GA9919-WT2

description: 2nd experiment


title: KZ1301_GB1033-WT1

description: 1st experiment


title: D6_PMN_130_Gent_T0_20181108


title: KZ1160_GA9918-WT1

description: 2nd experiment


title: KZ1038_GA8426-Tgfbr2KO2

description: 1st experiment


title: D6_PMN_130_Ceft_T0_20181108


title: D6_PMN_130_Azit_T1_20181108


title: D6_PMN_130_Azit_T0_20181108


title: KZ1038_GA8425-Tgfbr2KO1

description: 1st experiment


title: KZ1038_GA8424-WT2

description: 1st experiment


title: D55_PMN_H041_T1_20190110


title: 5-3

city: Shanghai

first: Qianqian

last: YIN

address: Chongqing South Road

department: Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

description:
processed data file: FPKM_processed_data_file.xlsx
processed data file: Normalized_processed_data_file.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was calculated, and then normalized with TMM standard; DESeq2 software was used to filter differentially expressed genes, according to the standard that |log2(fold change)|>=1 and P value <=0.05.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKM_processed_data_file.xlsx: Excel file includes FPKM values. S_5_1, S_5_2, and S_5_3 refer to 5mM lidocaine hydrochloride-treated samples; G1 is the mean value of the normalized ctr group (3 biological replications) values; G2 is the mean value of the normalized lidocaine group (3 biological replications) values.
Supplementary_files_format_and_content: Normalized_processed_data_file.xlsx: Excel file includes normalized values. S_5_1, S_5_2, and S_5_3 refer to 5mM lidocaine hydrochloride-treated samples; G1 is the mean value of the normalized ctr group (3 biological replications) values; G2 is the mean value of the normalized lidocaine group (3 biological replications) values.

organism: Rattus norvegicus

source_name: dorsal root ganglion neurons

growth_protocol: Primary DRG neurons single cell suspension were isolated from SD rat dorsal root ganglions (120g body weight, all DRGs), and cultured with neurobasal medium (B-27 supplemented) at 37℃.

extract_protocol:
Total RNA were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Neurons were treated with or without 5mM lidocaine hydrochloride for 24 hours.

value: Sprague Dawley

value: Dorsal root ganglion neurons

tag: passage

value: Primary culture

tag: treatment

value: Lidocaine


title: 5-2


title: D55_PMN_H041_T0_20190110

value: Co-culture

value: PMN


title: KZ1038_GA8423-WT1

description: 1st experiment


title: D55_PMN_H041_Gent_T1_20190110

value: 60 min in medium with PMN


title: D55_PMN_H041_Gent_T0_20190110


title: 5-1


title: D55_PMN_H041_Ceft_T1_20190110


title: D55_PMN_H041_Ceft_T0_20190110


title: Ctr-3


title: H40-8-C_NDME13348

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with High in the column of processed data file

data_processing:
we predicted the open reading frames (ORFs) for gene catalogue of 14 samples using PROKKA pipeline.The high-quality reads from each sample were used as input data for MetaPhlAn2 , a tool to characterize the composition of microbial communities.
Genome_build: mm10
Supplementary_files_format_and_content: Abundance of taxonomic annotation.txt

source_name: cecum contents

extract_protocol:
the mouse cecum contents were collected into 1.5 ml sterile microcentrifuge tubes separately, then sent to Novogene Co. Ltd. (Beijing, China) at low temperatures quickly after liquid nitrogen flash freezer.
Metagenomic DNA was extracted using standard protocol by Novogene Co. Ltd. There were about three indicators to evaluate DNA samples quality: purity, concentration and the degree of degradation. After quality control (QC) for DNA, 1 μg DNA in each sample was prepared for generating sequence libraries using NEBNext Ultra DNA Library Prep Kit. First, the DNA sample was fractured to a length of approximately 300 base pairs by ultrasonication, then the DNA fragments were amplified by PCR. Finally, the qualified library preparations were sequenced on an Illumina HiSeq2500 platform and pair-ended reads were generated for each sample.

tag: tissue

value: cecum contents (gut microbiota)

tag: developmental stage

value: 6 weeks

value: Zearalenone

tag: dose

value: 40μg/kg/ bw/day for 2 weeks


title: Ctr-2


title: H40-6-C_NDME13347


title: H40-4-C_NDME13346


title: D55_PMN_H041_Azit_T1_20190110

value: Azit


title: D55_PMN_3X130_T1_20190129


title: Ctr-1


title: D55_PMN_H041_Azit_T0_20190110

value: 0 min in medium with PMN


title: D55_PMN_3X130_T0_20190129


title: D55_PMN_3X130_Gent_T0_20190129

value: Gent


title: D55_PMN_3X130_Gent_T1_20190129


title: D55_PMN_3X130_Ceft_T1_20190129


title: D60_PMN_alone_T0_20190730

value: PMN alone

value: 0 min in medium alone


title: H40-1-C_NDME13344


title: PTC 2

description: tRNA

tag: diagnosis

value: Papillary thyroid cancer (PTC)

value: serum

tag: age

tag: Sex

value: female

tag: thyroiditis

value: yes


title: D55_PMN_3X130_Ceft_T0_20190129

tag: antibiotic

value: Ceft


title: D60_PMN_alone_T1_20190416

value: 60 min in medium alone


title: D6_PMN_H041_T1_20190122

value: Co-culture

value: PMN


title: D55_PMN_3X130_Azit_T0_20190129


title: L20-5-C_NDME13343

description: The group information is prefixed with Low in the column of processed data file

tag: strain

value: cecum contents (gut microbiota)

value: 20μg/kg/ bw/day for 2 weeks


title: D60_PMN_alone_T0_20190416


title: L20-4-C_NDME13342

value: 6 weeks

value: Zearalenone


title: D55_PMN_130_T1_20181106

value: 60 min in medium with PMN

value: Opaless


title: D55_PMN_3X130_Azit_T1_20190129

value: Azit


title: D55_PMN_130_T0_20181106

value: 0 min in medium with PMN


title: D6_PMN_alone_T1_20190416

value: PMN alone


title: H40-3-C_NDME13345

value: 40μg/kg/ bw/day for 2 weeks


title: D55_PMN_130_Gent_T1_20181106

value: Gent


title: D55_PMN_130_Ceft_T0_20181106


title: L20-2-C_NDME13340


title: L20-3-C_NDME13341


title: D55_PMN_130_Gent_T0_20181106


title: D55_PMN_130_Ceft_T1_20181106


title: D55_PMN_130_Azit_T1_20181106


title: L20-1-C_NDME13339


title: D55_PMN_130_Azit_T0_20181106


title: D60_H041_T1_20190709

organism: Neisseria gonorrhoeae

value: Bacteria alone


title: D6_PMN_alone_T0_20180802

value: 0 min in medium alone


title: D6_PMN_3X130_T1_20190307


title: Con-8-C_NDME13338

description: The group information is prefixed with Control in the column of processed data file

value: control


title: D60_H041_Gent_20190709

value: 60 min in medium alone


title: Con-4-C_NDME13337


title: D60_H041_Azit_20190709


title: D60_PMN_3X130_Ceft_T1_20190305

value: Co-culture

value: Ceft


title: D60_3X130_T1_20190305


title: Con-3-C_NDME13336

value: cecum contents (gut microbiota)


title: D60_3X130_Ceft_20190305


title: D55_PMN_alone_T0_20190416

value: PMN


title: D60_H041_Ceft_20190709


title: D6_PMN_alone_T1_20180802


title: D60_3X130_Azit_20190305


title: Con-1-C_NDME13334

value: 6 weeks


title: Con-2-C_NDME13335


title: WM9 NME1-EGFP clone 21 NME1-Low.3

first: David

middle: M

last: Kaetzel

address: 108 N Greene St

department: Biochemistry and Molecular Biology

institute: University of Maryland, Baltimore

data_processing:
Strand-specific paired-end Illumina libraries were mapped to the Human reference, Ensembl release GRCh38.92, using HiSat2 v2.0.4, with default mismatch parameters.
Read counts for each annotated gene were calculated using HTSeq
The DESeq Bioconductor package (v1.5.24) was used to estimate dispersion, normalize read counts by library size to generate the counts per million for each gene, and determine differentially expressed genes between high and low samples.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Differentially expressed transcripts with a FDR ≤ 0.05 and log2 fold change ≥ 1.0 were used for downstream analyses.
Genome_build: GRch38.92
Supplementary_files_format_and_content: tab delimited text files

source_name: WM9 NME1-EGFP melanoma cell line - clone 21

growth_protocol: WM9 NME1-EGFP clone 21 cells were grown on uncoated 15cm corning dishes. The cells were grown at 5% CO2 at 37degC in TU2% media. Media consists of a 4:1 (v/v) ratio of MCDB:Leibovitz L-15 media (Sigma-Aldrich) and 0.1% (v/v) sodium bicarbonate (Gibco), supplemented with 2mM CaCl2, 2.5ug/ml insulin, and 2% FBS (Gibco) and set to pH 7.2.

extract_protocol:
Total RNA was extracted with Rneasy Mini Kit (Qiagen 74106) and was subjected to Dnase treatment (Qiagen 79254)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were removed from the dish with 0.05% trypsin. The trypsin reaction was quenched with TU2% media. Cells were pelleted at 100g for 3 min and washed with PBS prior to resuspension with PBS + 2% FBS. Cells wre sorted on BD Areai II into 5mL polystrene round-botto FACS tubes containing PBS + 10% FBS

tag: cell type

value: Metastatic melanoma cell line

tag: passages


title: D6_PMN_alone_T0_20190416

data_processing:
Neisseria gonorrhoeae: Sequence reads were trimmed for adaptor sequence and mapped to the Opaless_3X or H041  Neisseria genomes using bowtie v1.0 with parameters -mode=v --num_mismatches=2 --file-type=fastq --seedlen=28 --minins=0 --maxins=600 --library-type=fr  --args='--sam' --v --gzip
Homo sapiens: Sequenced reads were trimmedfor adaptor sequence and mapped to the 2018 GRCh38 Human genome assembly using HISAT v2.0 with parameters -mismatch-penalties=6,2 --softclip-penalties=2,1 --read-gap-penalties=5,3 --ref-gap-penalties=5,3 --min-intronlen=20 --max-intronlen=500000 --score-min=L,0,-0.2 --pen-cansplice=0 --num-threads=1 --pen-noncansplice=12 --pen-canintronlen=G,-8,1 --pen-noncanintronlen=G,-8,1 --rna-strandness=RF --dta-cufflinks=1 --num-alignments=5 --minins=0 --maxins=600 --no-unal=1 --args='' --v
Neisseria gonorrhoeae: Reads Per Kilobase per Million values for gene features were calculated as described in Shenoy et al. PLoS Pathog. 2017 Aug 25;13(8):e1006582. doi: 10.1371/journal.ppat.1006582. eCollection 2017 Aug.
Homo sapiens: Reads Per Kilobase per Million values for exon features were calculated as described in Shenoy et al. PLoS Pathog. 2017 Aug 25;13(8):e1006582. doi: 10.1371/journal.ppat.1006582. eCollection 2017 Aug.
Genome_build: All data derived from the Opaless and Opaless_3X strains have been mapped to the Opaless_3X genome (GenBank Accession: WHPL00000000), while data derived from the H041 strain have been mapped to the H041 genome (GenBank Accession: WHPH00000000). All human data were mapped to 2018 GRCh38 Human genome assembly.

tag: donor

tag: treatment condition


title: D55_PMN_alone_T1_20180920

tag: human cell type

tag: incubation time


title: WM9 NME1-EGFP clone 21 NME1-Low.2


title: D55_PMN_alone_T1_20190416

tag: n. gonorrhoeae strain


title: IP CHAT_WT_SALINE Rep4

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
polysome bound mRNA
Pooled 4 animals, 14 d osmotic minipump, saline
1094_Chat_IP_CHAT_WT_SALINE_Rep4_CTTGTA_L003

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC mm10 whole genome using STAR version 2.3.0e_r291, with default settings.
Quantification of aligned reads was done using htseq-count module, part of the ‘HTSeq’ framework, version 0.6.0, using default settings, with ‘union’ mode to handle reads overlapping more than one feature.
Differentially expressed genes were identified by performing a negative binomial test using DESeq2 (R-package version 1.4.5) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files include counts

source_name: Medial Habenula

growth_protocol: All mice were maintained on a 12h light-dark cycle with ad lib access to food and water. Adult mice were used for all experiments (>8 weeks of age).

extract_protocol:
Brain regions of interest were microdissected, and homogenized immediately for IP using magnetic beads conjugated to anti-GFP. Total RNA was extracted from both the total homogenate (INPUT) and the IP fraction.
Ovation RNA-Seq System V2 kit (Nugen, Cat# 7102) was used with 10ug of RNA for MHb samples or 500pg of RNA for IPN samples for generation of SPIA cDNA. 1ug of SPIA cDNA was fragmented to 250bp before proceeding with library prepartion using the TruSeq DNA Nano LT Sample Prep Kit (Illumina, Cat# 20015964).

treatment_protocol: Animals were sacrificed by live decapitation, brains were rapidly removed and regions of interest dissected on ice. See sample details for specific drug treatments.

value: Medial Habenula

tag: background strain

tag: transgene(s)

value: ChAT-TRAP (DW167)

tag: fraction

value: Immunopurified (IP)


title: IP CHAT_WT_SALINE Rep3

description:
polysome bound mRNA
Pooled 4 animals, 14 d osmotic minipump, saline
1093_Chat_IP_CHAT_WT_SALINE_Rep3_GCCAAT_L003

tag: tissue


title: D60_130_Gent_20181113

extract_protocol:
At indicated times, samples were placed on ice. Bacteria alone were collected into microcentrifuge tubes, pelleted, and stored in RNAprotect at -80C. Supernatants were discarded from neutrophil containing samples, RNA protect was added, and samples were stored at -80C. Samples were exposed to EDTA pre-extraction and during the lysis step. Extractions were performed using Qiagen’s RNeasy extraction kit as per manufacturer’s protocol. An additional Turbo DNase was performed after the final step of RNeasy protocol. Quality and quantity were determined using the Agilent 4200 TapeStation System.
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

value: Opaless


title: D60_130_T1_20181113


title: D60_3X130_Gent_20190305


title: WM9 NME1-EGFP clone 21 NME1-High.3


title: D60_130_Azit_20181113

value: Azit


title: WM9 NME1-EGFP clone 21 NME1-High.2


title: D60_PMN_3X130_Ceft_T1_20190730

value: 60 min in medium with PMN


title: WM9 NME1-EGFP clone 21 NME1-Low.1


title: D6_H041_T1_20190122


title: INPUT MHb-Saccharin-Saline

description:
total RNA
Pooled 4 animals, 0.2% saccharin in drinking water x 6 weeks, i.p. saline 3 hr before tissue collection
824_Chat_INPUT-MHb-Saccharin-Saline_GCCAAT_L008

value: Input


title: WM9 NME1-EGFP clone 21 NME1-High.1


title: Input right_MHb

description:
total RNA
Pooled 9 males, Right MHb
823_Chat_Input_right_MHb_ACAGTG_L003


title: D6_H041_Gent_20190122

value: Bacteria alone

value: Gent


title: D6_H041_Ceft_20190122


title: Saccharin_saline input2

description:
total RNA
Pooled 4 animals, 0.2% saccharin in drinking water x 6 weeks, i.p. saline 3 hr before tissue collection
741_Chat_Saccharin_saline_input2_GCCAAT_L002


title: Input left_MHb

description:
total RNA
Pooled 9 males, Left MHb
821_Chat_Input_left_MHb_GCCAAT_L007


title: IP CHAT_WT_SALINE Rep2

description:
polysome bound mRNA
Pooled 4 animals, 14 d osmotic minipump, saline
1092_Chat_IP_CHAT_WT_SALINE_Rep2_GCCAAT_L001


title: D6_H041_Azit_20190122


title: D60_130_Ceft_20181113


title: black684_control

city: Durham

first: Vincent

middle: Michael

last: Perez

state: NC

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

description: mRNA isolated using using Illumina TruSeq® RNA sample preparation kit

data_processing:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: GRCm38, mus_musculus_mm10
Supplementary_files_format_and_content: FPKM, readcounts

source_name: whole liver

growth_protocol: Mice were maintained on a standard chow diet from the ages of 5 to 11 weeks. After 11 weeks, the mice were CO2 asphyxiated, sacrified, and dissected for organ harvesting.

extract_protocol:
RNA was isolated using standard QIAzol protocol (Cat No./ID 79306). After RNA isolation, we cleaned up the RNA using the Qiagen RNeasy kit following the manufacturer’s protocol (Cat No./ID 74104). Quality control checks of the RNA were performed to define purity and concentration. We used a nanodrop to assess the quantity and quality for each sample, ensuring the quantity was between 50-250ng/µl and the 260/280 was between 1.95-2.10. We ensured no RNA degradation occurred using Agarose Gel Electrophoresis for each sample. Lastly, before sequencing Novogene performed additional quality and quantity assessments of the RNA samples using an Agilent 2100 instrument and gel electrophoresis.
RNA-Seq libraries were prepared using Illumina TruSeq® RNA sample preparation kit as per the manufacturer’s protocol. Library construction, additional quality assessment, and sequencing were performed by Novogene Corporation, Ltd. Library concentration was quantified with a Qubit 2.0 fluorometer from Life Technologies and samples diluted to 1ng/µL before checking insert size using a bioanalyzer (Agilent 2100 Bioanalyzer) and quantifying to greater accuracy using qPCR. Using paired-end sequencing at a depth of 40 million reads or greater per sample was completed on final libraries.
We used paired-end sequencing for RNA-sequencing experiments.

treatment_protocol: Liver slices (70mg) snap frozen in RNAlater® were thawed on ice, transferred to a 2mL tubes with 1mL of QIAzol, and thoroughly homogenized.

value: liver

value: 11 weeks

value: female

tag: genotype

value: wildtype control


title: 552_Pool2-Chat-Su-Input_GCCAAT_L006

description:
total RNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
552_Pool2-Chat-Su-Input_GCCAAT_L006


title: black676_control

tag: age


title: black659_control

tag: Sex


title: black656_control


title: D6_3X130_T1_20190307

source_name: Neisseria gonorrhoeae strains FA1090 derivatives/H041 and adherent primary human neutrophils, alone and after co-culture over time, with or without prior antibiotic treatment

value: 60 min in medium alone


title: chat_NW_2nd_GCCAAT_L008

description:
polysome bound mRNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
476_chat_NW_2nd_GCCAAT_L008


title: black652_fatp2KO


title: D6_3X130_T1_20180802


title: D55_PMN_alone_T0_20180920

value: PMN alone

value: PMN

value: 0 min in medium alone


title: black634_fatp2KO


title: D6_3X130_Ceft_20190307

value: Ceft


title: chat_NT_2nd_ACAGTG_L007

description:
polysome bound mRNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
474_chat_NT_2nd_ACAGTG_L007

value: Medial Habenula

value: ChAT-TRAP (DW167)


title: 473_Pool1-Chat-NT-IP_ACAGTG_L005

description:
polysome bound mRNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
473_Pool1-Chat-NT-IP_ACAGTG_L005

value: Immunopurified (IP)


title: S24_ALK knockdown_alectinib_24h_rep3

city: Heidelberg

first: Anne

last: Berberich

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description:
SAMPLE 12
S24_primary glioblastoma cell culture_ALK knockdown_alectinib treatment_rep3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization

label_protocol: Standard Illumina label protocol

growth_protocol: Cells were cultured in neurosphere medium (DMEM/F12 medium (Life Technologies, Carlsbad, USA) supplemented with B27 supplement, heparin (5 µg/ml), basic fibroblast growth factor (bFGF) (20 ng/ml) and epidermal growth factor (EGF) (20 ng/mL).

extract_protocol: Total RNA was isolated using the Qiagen RNAeasy RNA Isolation Kit (Qiagen, Hilden Germany).

treatment_protocol: Cells were treated for 24h with 500nM alectinib or respective DMSO amounts as control treatment

tag: cell line

value: glioblastoma cells

value: ALK knockdown

tag: treatment

value: alectinib


title: chat_SU_2nd_CTTGTA_L008

description:
polysome bound mRNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
472_chat_SU_2nd_CTTGTA_L008


title: black643_fatp2KO


title: Quiescent_44

city: Stellenbosch

first: Hugh

last: Patterton

address: Merriman Street

department: Center for Bioinformatics and Computational Biology

country: South Africa

institute: Stellenbosch University

description: PCR-amplified barcode fragment

data_processing:
The number of times that each barcode sequence was present in the FASTQ file was assessed for “up” and “down” barcodes with "get_seqs_from_fastq" for each time point, quantitated with "match_barcodes_to_strain", and the average of the “up” and “down” value, adjusted for the amplified DNA signal, expressed as the log2 ratio relative to the level in the mixed starting population. The code is available at github.com/hpatterton.
Supplementary_files_format_and_content: Processed data file contains 4 columns: barcode up, counts, barcode down, counts.  The barcodes refer to that specified in Dai, J. et al. Probing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants. Cell 134, 1066–1078 (2008). Each row contains the matching up and down barcodes for a given histone mutant strain.

organism: Saccharomyces cerevisiae

source_name: Stationary phase cells

growth_protocol: The histone H3 and H4 mutant library was replica plated onto omnitray YPD-agar plates, and selected with 200 ng/ml nourseothricin (Sigma) antibiotic. Colonies were grown for 2-3 days at 30°C. Slow-growing colonies were separately streaked out from the original stock, and grown for 2-3 days at 30°C. The contents of all the plates, including the slow-growers (equivalent volume of a normal colony) were scraped off, and pooled in a 50 ml conical centrifuge tube containing YPD liquid media with 200 ng/ml nourseothricin. The pooled culture was diluted to a final concentration of OD600 = 50, 15% (v/v) glycerol was added, and stored as aliquots at -80°C.  The pooled culture was inoculated into 100ml YPD liquid media to a final concentration of OD600 ~ 0.003. Cells were grown with rotary shaking (180 rpm) at 30°C for approximately 10 generations (~15 h).  The pooled culture was then further diluted to OD600 of 0.06 in 250 ml YPD liquid media, and incubated for up to 60 d with continual shaking (180 rpm) at 30°C. Aliquots (10 ml) were recovered at the times indicated.

extract_protocol: DNA polymerase (Roche), 0.4 ul of 100 uM “up” or “down” barcode primer pair, 0.5 ul of 10 mM dNTP, 12 ul of 25 mM MgCl2, 3 ul of 10x PCR buffer without MgCl2, and water to in a final volume of 30 ul. The primer sequences were ATGTCCACGAGGTCTCT, CCTCGACCTGCAGCGTA, CGGTGTCGGTCTCGTAG, and CCCAGCTCGAATTCATC for “up”, forward and reverse, and “down”, forward and reverse, respectively.  The amplified DNA was purified, quantitated, single-end adapters with index primers (Illumina) ligated to each sample, and single-end sequenced on a HiSeq 2500 (ARC Biotechnology Platform, University of Pretoria).

tag: strain

value: JDY86 derived

tag: incubation time (days)

value: quiescent


title: Non-quiescent_44

description: PCR-amplified barcode fragment

tag: cell type

value: non-quiescent


title: S24_alectinib_24h_rep3

description:
SAMPLE 6
S24_primary glioblastoma cell culture_alectinib treatment_rep3

value: control


title: S24_ALK knockdown_control_24h_rep3

description:
SAMPLE 9
S24_primary glioblastoma cell culture_ALK knockdown_DMSO control treatment_rep3


title: S24_ALK knockdown_control_24h_rep1

description:
SAMPLE 7
S24_primary glioblastoma cell culture_ALK knockdown_DMSO control treatment_rep1


title: S24_ALK knockdown_alectinib_24h_rep1

description:
SAMPLE 10
S24_primary glioblastoma cell culture_ALK knockdown_alectinib treatment_rep1


title: 475_Pool1-Chat-NW-IP_GTGAAA_L005

description:
polysome bound mRNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
475_Pool1-Chat-NW-IP_GTGAAA_L005


title: black631_fatp2KO

value: liver

value: 11 weeks

value: female


title: Quiescent_34

description: PCR-amplified barcode fragment


title: S24_ALK knockdown_control_24h_rep2

description:
SAMPLE 8
S24_primary glioblastoma cell culture_ALK knockdown_DMSO control treatment_rep2


title: S24_ALK knockdown_alectinib_24h_rep2

description:
SAMPLE 11
S24_primary glioblastoma cell culture_ALK knockdown_alectinib treatment_rep2


title: S24_control_24h_rep2

description:
SAMPLE 2
S24_primary glioblastoma cell culture_DMSO control treatment_rep2


title: D6_3X130_Azit_20190307

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

institute: University of Maryland School of Medicine

tag: donor

value: Bacteria alone

value: 60 min in medium alone

tag: antibiotic

value: Azit


title: S24_alectinib_24h_rep1

description:
SAMPLE 4
S24_primary glioblastoma cell culture_alectinib treatment_rep1


title: 471_Pool2-Chat-Su-IP_CTTGTA_L006

description:
polysome bound mRNA
Pooled 4 animals, 2% sucrose in drinking water x 6 weeks
471_Pool2-Chat-Su-IP_CTTGTA_L006


title: D6_3X130_Gent_20190307

tag: treatment condition

value: Gent


title: Non-quiescent_34

description: PCR-amplified barcode fragment


title: black675_control

description: mRNA isolated using using Illumina TruSeq® RNA sample preparation kit

value: male

value: wildtype control


title: Gpr151-WT-IP-2nd_CTTGTA_L005

description:
polysome bound mRNA
Pooled 4 animals, baseline
467_Gpr151-WT-IP-2nd_CTTGTA_L005

value: Medial Habenula

value: ChAT-TRAP (DW167)

value: Immunopurified (IP)


title: D6_130_T1_20181108

tag: incubation time

value: Opaless


title: D6_3X130_Azit_20190619

tag: n. gonorrhoeae strain


title: Quiescent_24

description: PCR-amplified barcode fragment

value: JDY86 derived


title: S24_control_24h_rep3

description:
SAMPLE 3
S24_primary glioblastoma cell culture_DMSO control treatment_rep3

value: glioblastoma cells


title: S24_control_24h_rep1

description:
SAMPLE 1
S24_primary glioblastoma cell culture_DMSO control treatment_rep1


title: S24_alectinib_24h_rep2

description:
SAMPLE 5
S24_primary glioblastoma cell culture_alectinib treatment_rep2

value: alectinib


title: D6_130_Gent_20181108


title: chat_contral_CTTGTA_L006

description:
polysome bound mRNA
Pooled 4 animals, baseline
465_chat_contral_CTTGTA_L006

tag: background strain


title: Non-quiescent_24

description: PCR-amplified barcode fragment

value: non-quiescent


title: black662_control

value: liver


title: D6_130_Ceft_20181108

value: Ceft


title: D6_130_Azit_20181108


title: black695_control

value: 11 weeks


title: black655_control


title: black693_fatp2KO


title: Non-quiescent_14

description: PCR-amplified barcode fragment


title: Quiescent_14

description: PCR-amplified barcode fragment

value: quiescent


title: D55_H041_T1_20190110

value: Bacteria alone

value: 60 min in medium alone


title: Quiescent_7

description: PCR-amplified barcode fragment


title: Pool-R-drd1-1-WT-t-2_GCCAAT_L003

description:
total RNA
WT control
135_Pool-R-drd1-1-WT-t-2_GCCAAT_L003

source_name: Striatum

value: Striatum

tag: transgene(s)

value: Drd1-TRAP (CP73)

value: Input


title: Gpr151-WT-IP_ACAGTG_L002

description:
polysome bound mRNA
Pooled 4 animals, baseline
463_Gpr151-WT-IP_ACAGTG_L002

value: Medial Habenula

tag: fraction


title: Pool-S-drd1-1-WT-t-3_GCCAAT_L004

description:
total RNA
WT control
136_Pool-S-drd1-1-WT-t-3_GCCAAT_L004

tag: tissue


title: D55_H041_Gent_20190110

value: Gent


title: black650_fatp2KO

value: male

tag: genotype


title: Non-quiescent_7

description: PCR-amplified barcode fragment


title: D55_H041_Ceft_20190110


title: black629_fatp2KO

tag: age


title: D55_H041_Azit_20190110

value: Azit


title: 19_KIN-KIN

city: Montpellier

first: Marion

last: de Toledo

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS UMR5535

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Trim Galore was used to perform adapter trimming and quality control in two subsequent steps. The 2 additional bases that contain a cytosine which was artificially introduced at the end-repair step during the library preparation (--rrbs option) were  removed.
The mm9 mouse reference genome was prepared for Bismark using bismark_genome_preparation script. Bismark software (version 0.17.0) from the Babraham Institute was used to align trimmed RRBS reads to the mouse genome.
Then, bismark_methylation_extractor script extracted the methylation call for every single C analysed.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text file with columns ID, chromosome, start, strand, coverage, frequency methylated, frequency non-methylated

source_name: islets of Langherans isolated from lmna LCS mice

growth_protocol: Mice were housed under a 12-h light/dark cycle and given an ad libitum regular chow diet (A04; Safe)

extract_protocol:
Total DNA was purified from isolated islets using MasterPureTM Complete DNA and RNA Purification kit
RRBS libraries were prepared with the 'Premium RRBS kit' (Diagenode) according to the manufacturer's instructions.

treatment_protocol: Islets were isolated from 70 week old mice

value: islets of Langerhans

value: 70 weeks old


title: black638_fatp2KO

tag: Sex


title: Quiescent_5

description: PCR-amplified barcode fragment

value: JDY86 derived


title: Non-quiescent_5

description: PCR-amplified barcode fragment

value: non-quiescent


title: H3K27me3-35S-COLDAIR-rep2_ChIP-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.2.6 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using SICER v 1.1 with the following setting: window size 200,  gap size 200, E-value 100, FDR 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig

source_name: Arabidopsis seedlings

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Arabidopsis seedlings


title: H3K27me3-35S-COLDAIR-rep1_ChIP-seq


title: 18_WT

source_name: islets of Langherans isolated from wt mice


title: Quiescent_3

description: PCR-amplified barcode fragment


title: D55_3X130_T1_20190129


title: 17_WT


title: D55_3X130_Gent_20190129


title: Non-quiescent_3

description: PCR-amplified barcode fragment


title: D55_3X130_Ceft_20190129

value: Ceft


title: H3K27me3-Col-0-rep2_ChIP-seq


title: H3K27me3-Col-0-rep1_ChIP-seq


title: R1970wt

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Alignment was performed with TopHat 2.1.1 (with Bowtie 2.2.9) to the mm9 version of the Mus muculus genome. The transcript annotation was retrieved from UCSC on August 31, 2017.
Counting of reads aligned to a gene was performed with HTSeq-count 0.9.0
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text file. First column is the gene identifier (gene symbol), the following columns are the raw counts (non-normalized) for each sample.

extract_protocol:
Total RNA was extracted from isolated islets using TRIzol (Life Technologies, USA)
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.


title: Quiescent_2

description: PCR-amplified barcode fragment


title: D55_3X130_Azit_20190129


title: R270wt


title: R370wt


title: D55_130_T1_20181106

value: Opaless


title: Quiescent_1

description: PCR-amplified barcode fragment

value: quiescent


title: 20_KIN-KIN


title: Pool-Q-drd1-1-WT-t-1_GCCAAT_L002

description:
total RNA
WT control
134_Pool-Q-drd1-1-WT-t-1_GCCAAT_L002


title: Non-quiescent_2

description: PCR-amplified barcode fragment


title: H3K4me3-35S-COLDAIR-rep1_ChIP-seq


title: D55_130_Gent_20181106

value: Bacteria alone


title: H3K4me3-35S-COLDAIR-rep2_ChIP-seq


title: R2270KIKI


title: Non-quiescent_1

description: PCR-amplified barcode fragment


title: D55_130_Ceft_20181106

value: 60 min in medium alone


title: Quiescent_0

description: PCR-amplified barcode fragment


title: D55_130_Azit_20181106


title: H3K4me3-Col-0-rep1_ChIP-seq


title: H3K4me3-Col-0-rep2_ChIP-seq


title: Non-quiescent_0

description: PCR-amplified barcode fragment


title: Cortical neurons, Anta_R5

status: Public on Nov 08 2019

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Read trimming with Skewer and alignment with Bowtie.
Peak calling with MACS2 (-q 0.1 -g mm).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak (peak coordinates determined with MACS2)

source_name: cortical neurons in vitro differentiated for 7 days, treated with Antagonist for cannabinoid receptort signaling, replicate 5

growth_protocol: Cerebral tissues (cortex/hippocampus) of mouse embryos were isolated at E18.5 and plated for 7 days in vitro.

extract_protocol:
Cells were pelleted and lysed in a buffer containing Digitonin and transposase enzyme. After transposition the DNA was purified.
The purified samples were enriched using index primers and purified librareies were quality checked and sequenced on Illumina HiSeq 3000/4000 instruments.

treatment_protocol: Cultures were exposed to Agonist (2-AG), or to Antagonist (AM251) of the cannabinoid receptor 1  for 7 days.

value: brain

value: WT

value: Anta


title: Cortical neurons, Anta_R6

source_name: cortical neurons in vitro differentiated for 7 days, treated with Antagonist for cannabinoid receptort signaling, replicate 6


title: Cortical neurons, Ago_R6

source_name: cortical neurons in vitro differentiated for 7 days, treated with Agonist for cannabinoid receptort signaling, replicate 6

value: Ago


title: Cortical neurons, Ago_R5

source_name: cortical neurons in vitro differentiated for 7 days, treated with Agonist for cannabinoid receptort signaling, replicate 5


title: Cortical neurons, UT_R5

source_name: cortical neurons in vitro differentiated for 7 days, untreated, replicate 5

value: UT


title: Cortical neurons, UT_R6

source_name: cortical neurons in vitro differentiated for 7 days, untreated, replicate 6

value: male


title: Cortical neurons, Ago_R4

source_name: cortical neurons in vitro differentiated for 7 days, treated with Agonist for cannabinoid receptort signaling, replicate 4


title: Cortical neurons, Anta_R4

source_name: cortical neurons in vitro differentiated for 7 days, treated with Antagonist for cannabinoid receptort signaling, replicate 4


title: Cortical neurons, Ago_R3

source_name: cortical neurons in vitro differentiated for 7 days, treated with Agonist for cannabinoid receptort signaling, replicate 3


title: Cortical neurons, UT_R4

source_name: cortical neurons in vitro differentiated for 7 days, untreated, replicate 4


title: Cortical neurons, Ago_R1

source_name: cortical neurons in vitro differentiated for 7 days, treated with Agonist for cannabinoid receptort signaling, replicate 1


title: Cortical neurons, Ago_R2

source_name: cortical neurons in vitro differentiated for 7 days, treated with Agonist for cannabinoid receptort signaling, replicate 2


title: Cortical neurons, Anta_R1

source_name: cortical neurons in vitro differentiated for 7 days, treated with Antagonist for cannabinoid receptort signaling, replicate 1


title: Cortical neurons, UT_R3

source_name: cortical neurons in vitro differentiated for 7 days, untreated, replicate 3


title: Cortical tissue, embryo E18 - w6 5-7 (rrbs)

data_processing:
RRBS data were processed with RnBeads (Assenov et al. 2014)
Genome_build: mm10
Supplementary_files_format_and_content: BED (CpG coordinates with methylation levels)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with omega-6 enriched diet, replicate 3

extract_protocol:
Extracted DNA was subjected to the reduced representation bisulfite sequencing (RRBS) workflow
The purified samples were enriched using index primers and purified librareies were quality checked and sequenced on Illumina HiSeq 3000/4000 instruments.

treatment_protocol: Female C57BL/6 animals at 6 weeks of age were randomly assigned to either a hypercaloric diet enriched ~15-fold in ω-6 PUFAs while maintaining the ω-3:ω-6 PUFA ratio at 1:8 as in standard chow or to a standard diet. The effect of maternal diets on fetal brain development was evaluated at E18.5 after the "priming protocol" (consuming a high ω-6 PUFA diet starting 2 weeks prior to conception). Embryos were collected from pregnancies to keep the number of independent observations sufficient for statistical analyses and used for molecular biology.

tag: diet


title: Cortical neurons, UT_R1

source_name: cortical neurons in vitro differentiated for 7 days, untreated, replicate 1

tag: treatment


title: Cortical neurons, UT_R2

source_name: cortical neurons in vitro differentiated for 7 days, untreated, replicate 2

tag: strain


title: Cortical tissue, embryo E18 - w6 6-3 (rrbs)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with omega-6 enriched diet, replicate 2

growth_protocol: Female C57BL/6 animals at 6 weeks of age were randomly assigned to either a hypercaloric diet enriched ~15-fold in ω-6 PUFAs while maintaining the ω-3:ω-6 PUFA ratio at 1:8 as in standard chow or to a standard diet.


title: Cortical tissue, embryo E18 - Ctr 5-5 (rrbs)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with control diet, replicate 4

value: control


title: R2170KIKI

source_name: islets of Langherans isolated from lmna LCS mice

value: islets of Langerhans


title: R2070KIKI

value: 70 weeks old


title: Cortical tissue, embryo E18 - Ctr 5-4 (rrbs)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with control diet, replicate 3


title: Cortical tissue, embryo E18 - Ctr 6-1 (rrbs)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with control diet, replicate 1


title: Cortical tissue, embryo E18 - Ctr 6-2 (rrbs)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with control diet, replicate 2


title: 10 Total RNA Torin 3

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

description: Sample 10

data_processing:
Adapter sequences were clipped using fastx_clipper, part of the FASTX Toolkit 0.0.13, with the following parameters: -a AGATCGGAAGAGCACACGTCT -l 20 -c -n -v -Q33
Reads were trimmed using fastx_trimmer with the following parameters: -Q33 -f 1
Trimmed reads were mapped to O. dioica rRNA and tRNA sequences using bowtie2 version 2.1.0  with the following parameters: -L 20
Reads not mapping to rRNA or tRNA were mapped to the O.dioica reference genome using Tophat 2.0.13 and Genoscope gene model annotations with default parameters
The featureCounts function in the Rsubread R package was used to count reads mapping to exons and to summarise these at the gene level
Genome_build: 1_Assembly_reference_unmasked_v3.0.fa
Oikopleura gene model annotations are publicly available on the Genoscope genome browser site (http://www.genoscope.cns.fr/externe/GenomeBrowser/Oikopleura/ ) under Downloads. We used the gene model annotations, and transcript IDs, in the "Oikopleura_annot_v1.0.gff? file (under Downloads > annotations). These annotations were used both as a guide in aligning reads to the genome and for counting reads mapping to exons (summarised at the gene/transcript level).
Supplementary_files_format_and_content: Matrix of read counts for each gene/transcript (row names are Genoscope transcript IDs) and each sample (summing reads from four lanes (two lanes from two flow cells)

organism: Oikopleura dioica

source_name: Female animals

extract_protocol:
Total RNA was extracted using RNeasy. Ribosome protected fragments (RPFs) were extracted using the ARTSeq kit from epicentre using the using MicroSpin S-400 column option.  rRNA was depleted from all samples using RiboZero.
Libraries were prepared for sequencing using the ARTSeq kit from epicentre and the included indices were added for multiplex sequencing creating barcodes as follows: Sample 1 CTTGTA; Sample 2 GCCAAT; Sample 3 ATCACG; Sample 4 CGATGT; Sample 5 TTAGGC; Sample 6 ACAGTG; Sample 7 CAGATC; Sample 8 ACTTGA; Sample 9 TGACCA; Sample 10 GATCAG; Sample 11 TAGCTT; Sample 12 GGCTAC

treatment_protocol: Animals were placed into beakers of seawater containing normal algal food dose for day 6 and either 1 μM Torin 1 (treatment) or 1 μM DMSO (vehicle control). Animals were exposed to treatment and control for 1.5 hrs before being collected, washed, spun down and frozen in liquid nitrogen.

tag: drug treatment

value: Torin 1

value: Whole animal

tag: developmental stage

value: Day 6


title: 11 RPF DMSO 3

description:
Ribosome-protected RNA
Sample 11

value: DMSO


title: 12 RPF Torin 3

description:
Ribosome-protected RNA
Sample 12


title: Cortical neurons, Anta_R3

source_name: cortical neurons in vitro differentiated for 7 days, treated with Antagonist for cannabinoid receptort signaling, replicate 3


title: Cortical neurons, Anta_R2

source_name: cortical neurons in vitro differentiated for 7 days, treated with Antagonist for cannabinoid receptort signaling, replicate 2


title: 3 Total RNA DMSO 2

description: Sample 3


title: 9 Total RNA DMSO 3

description: Sample 9


title: 7 RPF DMSO 2

description:
Ribosome-protected RNA
Sample 7


title: 8 RPF Torin 2

description:
Ribosome-protected RNA
Sample 8


title: AZD4573 8 hrs. rep. 3

city: Waltham

first: Steven

middle: W

last: Criscione

address: 35 Gatehouse Drive

department: Oncology Bioinformatics

institute: AstraZeneca

description:
TR_8h_3
processed data file: AZD4573_timecourse_geneBYsample_counts.csv

data_processing:
The python toolkit bcbio: (https://bcbio-nextgen.readthedocs.io/en/latest/) was used to implement the RNA-seq analysis pipeline using human hg38 reference genome and hg38 Ensembl transcripts (Ensembl version 79). RNA-seq data was aligned to human hg38 reference genome using HISAT2 (ver. 2.0.5). Standard data quality metrics were determined using FastQC.
All experimental samples passed standard data quality metrics. Ensembl transcripts were directly quantified using Sailfish (ver. 0.10.1),2 and R package tximport was used to create a gene by sample count table.
A list of cancer associated genes was derived from the union of a variety of sources including the COSMIC Cancer Gene Census (ver. 87), as a point of emphasis for differential expression.
Differential gene expression analysis on the sample gene count table was done using Voom and Limma R package using a standard comparison of experimental contrasts. The analysis determines log2 fold changes and FDR for genes for each comparison. EdgeR package was used to convert gene counts to normalized abundances or log2 counts per million (CPM).
Genome_build: hg38 (GRCh38) & hg38 Ensembl transcripts
Supplementary_files_format_and_content: AZD4573_timecourse_geneBYsample_counts.csv: Gene by sample count table output from Sailfish. Note Sailfish outputs expected counts rather than true integer values which may present a challenge for some differential expression methods.

source_name: MCF7 cell-line

growth_protocol: Cell lines were purchased from DSMZ, ATCC, or ECACC and authenticated by the AstraZeneca Cell Bank using DNA fingerprinting short tandem repeat assays. All cell lines were cultured in distributor recommended media, incubated at 37oC/5% carbon dioxide, and used within 20 passages.

extract_protocol:
RNA isolation and cDNA conversion were conducted using RNeasy Mini (Qiagen) and High Capacity cDNA RT (Applied Biosystems) kits, respectively, following the manufacturers’ protocols.
RNA was used for cDNA library construction at Novogene using an NEBNext Ultra mRNA Library Prep Kit for Illumina according to the manufacturer’s protocol. Briefly, mRNA was enriched using oligo(dT) beads followed by first strand cDNA synthesis using random hexamer primers. Next, double-stranded cDNA library was constructed through a series of terminal repair, poly-adenylation, and sequencing adaptor ligations and finally size selection and PCR enrichment. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer, and qualified libraries were sequenced on an Illumina HiSeq 4000 Platform using a paired-end 150 run (2×150 bases). 30 million raw reads were generated from each library.

treatment_protocol: MCF7 cells were treated with vehicle or AZD4573 for short periods of time (0h, 4h, and 8h) at appropriate concentration for target engagement.

tag: cell line

tag: cell type

value: Breast cancer cell line

value: AZD4573 8 hrs


title: 5 RPF DMSO 1

description:
Ribosome-protected RNA
Sample 5


title: Cortical tissue, embryo E18 - w6 6-3A (rrbs)

source_name: cortical tissue from embryonic mouse brain. Embryos are from dams fed with omega-6 enriched diet, replicate 1


title: AZD4573 4 hrs. rep. 2

description:
TR_4h_2
processed data file: AZD4573_timecourse_geneBYsample_counts.csv

value: AZD4573 4 hrs


title: AZD4573 4 hrs. rep. 1

description:
TR_4h_1
processed data file: AZD4573_timecourse_geneBYsample_counts.csv


title: AZD4573 8 hrs. rep. 1

description:
TR_8h_1
processed data file: AZD4573_timecourse_geneBYsample_counts.csv


title: DMSO untreated control rep. 1

description:
UNTR_1
processed data file: AZD4573_timecourse_geneBYsample_counts.csv


title: DMSO untreated control rep. 2

description:
UNTR_2
processed data file: AZD4573_timecourse_geneBYsample_counts.csv


title: RNA-seq HA-WBM-1D2 rep4

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
processed data file: Lance-RAMOS.count
WBM-1D2-4

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Reads with mapping quality less than 10 were removed.
Peaks were called by MACS2.
Differential binding peaks were identified using DiffBind based on consensus peaks occurring at least two samples.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: one peak file per Sample
PRO-seq: text file with raw counts for promoter-proximal and gene body region, and density for gene body (ppc, gbc, gbd)
RNA-seq: tab-delimited text file include raw counts for each Sample

source_name: RNA-seq HA-WBM-1D2

growth_protocol: Ramos cells were maintained in RPMI1640 +10 % FBS, Pen/Strep, and 50 ug/ml Hygromycin B. Puromycin was added to 200 ng/ml for WT, WBM, and ∆264 cells.

extract_protocol:
Chromatin was clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
ChIP libraries were prepared according to New England Biolabs  instructions accompanying the NEBNext Ultar II DNA Library Prep Kit for Illumina (Part# E7645S). After adapter ligation DNA was PCR amplified with NEBNext Multiplex Oligos for Illumina (Part# E7335S and E7500S) for 16 cycles (HA ChIP) or 15 cycles (WDR5 ChIP). For RNA-seq, libraries  were prepared using Poly-A selected at Genewiz using their standard methods, and for PRO-Seq, libraries were made using RNA that was made through a biotin-run on reaction.Biotin-RNA was base hydrolyzed, and extracted. 3'-adaptors were ligated to ends and 5'caps were removed, repaired, and then 5'-adaptors were ligated as well. Purified and intact biotin-RNA containing adaptors was used in a reverase transcriptase reaction to generate cDNA and cDNA was used to amplify full library using NEB High Fidelity Phusion polymerase.RNA libraries were prepared using Poly-A selected RNA.

treatment_protocol: Cells were plated at 0.75 million in RPMI +10% FBS + Pen/Strep and treated with 20 nM 4-OHT for 24 h

value: Ramos

value: Burkitt's lymphoma cell line

tag: genotype/variation

value: Tumor derived WBM-HA

value: 48h post 4-OHT treatment


title: RNA-seq HA-WBM-1D2 rep3

description:
processed data file: Lance-RAMOS.count
WBM-1D2-3


title: 6 RPF Torin 1

description:
Ribosome-protected RNA
Sample 6


title: RNA-seq HA-WBM-1D2 rep1

description:
processed data file: Lance-RAMOS.count
WBM-1D2-1


title: RNA-seq HA-WBM-1D2 rep2

description:
processed data file: Lance-RAMOS.count
WBM-1D2-2


title: RNA-seq HA-∆264-1E9 rep3

description:
processed data file: Lance-RAMOS.count
delta264-1E9-3

source_name: RNA-seq HA-∆264-1E9

value: Tumor derived {delta}264-HA


title: 2 Total RNA Torin 1

description: Sample 2


title: 4 Total RNA Torin 2

description: Sample 4


title: RNA-seq HA-∆264-1E9 rep2

description:
processed data file: Lance-RAMOS.count
delta264-1E9-2


title: AZD4573 4 hrs. rep. 3

description:
TR_4h_3
processed data file: AZD4573_timecourse_geneBYsample_counts.csv


title: 1 Total RNA DMSO 1

description: Sample 1


title: AZD4573 8 hrs. rep. 2

description:
TR_8h_2
processed data file: AZD4573_timecourse_geneBYsample_counts.csv


title: RNA-seq HA-∆264-1E9 rep1

description:
processed data file: Lance-RAMOS.count
delta264-1E9-1


title: RNA-seq HA-WT-3E7 rep3

description:
processed data file: Lance-RAMOS.count
WT-3E7-3

source_name: RNA-seq HA-WT-3E7

value: Tumor derived WT-HA


title: RNA-seq HA-WT-3E7 rep2

description:
processed data file: Lance-RAMOS.count
WT-3E7-2


title: DMSO untreated control rep. 3

description:
UNTR_3
processed data file: AZD4573_timecourse_geneBYsample_counts.csv